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Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD3

Organism
Vibrio fischeri (strain ATCC 700601 / ES114)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalytic activityi

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.UniRule annotation
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei5Purine nucleoside; shared with dimeric partnerBy similarity1
Binding sitei21Phosphate; via amide nitrogenBy similarity1
Binding sitei25PhosphateBy similarity1
Binding sitei44Phosphate; shared with dimeric partnerBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionGlycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciVFIS312309:G1G40-3722-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-typeUniRule annotation (EC:2.4.2.1UniRule annotation)
Short name:
PNPUniRule annotation
Gene namesi
Name:deoD3UniRule annotation
Ordered Locus Names:VF_A0968
OrganismiVibrio fischeri (strain ATCC 700601 / ES114)
Taxonomic identifieri312309 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
Proteomesi
  • UP000000537 Componenti: Chromosome II

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000631731 – 239Purine nucleoside phosphorylase DeoD-typeAdd BLAST239

Proteomic databases

PRIDEiQ5DYV8

Interactioni

Subunit structurei

Homohexamer.UniRule annotation

Protein-protein interaction databases

STRINGi312309.VF_A0968

Structurei

Secondary structure

1239
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 19Combined sources5
Helixi23 – 33Combined sources11
Beta strandi35 – 41Combined sources7
Helixi43 – 45Combined sources3
Beta strandi48 – 53Combined sources6
Beta strandi56 – 61Combined sources6
Helixi67 – 78Combined sources12
Turni79 – 81Combined sources3
Beta strandi85 – 94Combined sources10
Beta strandi104 – 112Combined sources9
Helixi116 – 120Combined sources5
Turni121 – 123Combined sources3
Helixi132 – 143Combined sources12
Beta strandi149 – 156Combined sources8
Helixi166 – 173Combined sources8
Beta strandi178 – 182Combined sources5
Helixi183 – 193Combined sources11
Beta strandi196 – 206Combined sources11
Turni207 – 210Combined sources4
Helixi215 – 235Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LDNX-ray1.48A1-239[»]
ProteinModelPortaliQ5DYV8
SMRiQ5DYV8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 91Phosphate bindingBy similarity4
Regioni180 – 182Purine nucleoside bindingBy similarity3
Regioni204 – 205Purine nucleoside bindingBy similarity2

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0813 LUCA
HOGENOMiHOG000274896
KOiK03784
OMAiFAMIADF
OrthoDBiPOG091H021M

Family and domain databases

HAMAPiMF_01627 Pur_nucleosid_phosp, 1 hit
InterProiView protein in InterPro
IPR004402 DeoD-type
IPR018016 Nucleoside_phosphorylase_CS
IPR000845 Nucleoside_phosphorylase_d
IPR035994 Nucleoside_phosphorylase_sf
PANTHERiPTHR43691:SF2 PTHR43691:SF2, 1 hit
PfamiView protein in Pfam
PF01048 PNP_UDP_1, 1 hit
SUPFAMiSSF53167 SSF53167, 1 hit
TIGRFAMsiTIGR00107 deoD, 1 hit
PROSITEiView protein in PROSITE
PS01232 PNP_UDP_1, 1 hit

Sequencei

Sequence statusi: Complete.

Q5DYV8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTPHINAPL DAFADTILMP GDPLRAKLIA ETYLENVVQV TDVRGMLGFT
60 70 80 90 100
GEFKGRKISV MGHGMGAPSA SIYFHELMTT YKVKNFIRIG SCGAIHDDVK
110 120 130 140 150
LKDLIVAIGA STDSKMNRIR FKDNDFAATA NYNMLSECVN TLKTTDINYL
160 170 180 190 200
VGNVFSSDLF YRPDEEQYDM MARYGILGVE MEVNALYSAA AENHCNAVAL
210 220 230
CTVTDHIKNH EHLTADERRT ELHEMINVAL DVALKLPTE
Length:239
Mass (Da):26,542
Last modified:March 15, 2005 - v1
Checksum:i0B35489AA6A19951
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000021 Genomic DNA Translation: AAW88038.1
RefSeqiWP_005423543.1, NC_006841.2
YP_206926.1, NC_006841.2

Genome annotation databases

EnsemblBacteriaiAAW88038; AAW88038; VF_A0968
GeneIDi3280781
KEGGivfi:VF_A0968
PATRICifig|312309.11.peg.3569

Similar proteinsi

Entry informationi

Entry nameiDEOD3_VIBF1
AccessioniPrimary (citable) accession number: Q5DYV8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 15, 2005
Last modified: May 23, 2018
This is version 75 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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